Changes in version 1.13.14 (2020-03-03)                 

Changes in existing functions

    o   inherits(a, b) is now used instead of class(a)==b.

                 Changes in version 1.13.6 (2020-01-03)                 

Changes in existing functions

    o   doSave was added to the combine.networks() function.

                 Changes in version 1.13.4 (2019-11-19)                 

Bug Fixes

    o   In the combine.networks() function, the netwok typo was fixed.

                Changes in version 1.11.34 (2019-10-21)                 

General

    o   The pipeline is now explained step by step in the vignette.

                Changes in version 1.11.32 (2019-10-18)                 

Changes in existing functions

    o   The Data argument of compute.pigengene can now be a matrix with
	only 1 column.

                Changes in version 1.11.30 (2019-10-02)                 

Changes in existing functions

    o   The doRetuNetworks argument is now added to the
	combine.networks function.

                Changes in version 1.11.28 (2019-10-01)                 

New functions

    o   message.if() is now exported.

                Changes in version 1.11.26 (2019-09-26)                 

Changes in existing functions

    o   Better QC in the gene.mapping() function, the possible keys
	will be printed if the input is not appropriate.

New functions

    o   save.if() is now exported.

                Changes in version 1.11.24 (2019-09-03)                 

Bug Fixes

    o   In the combine.networks() function, selectedModules does not
	need to be "All". Also, if saveFile=NULL, nothing will be saved
	without any error.

                Changes in version 1.11.20 (2019-05-15)                 

Changes in existing functions

    o   Data and Labels can now be lists, which will be combined using
	combine.networks() before analysis.

                 Changes in version 1.11.4 (2019-05-02)                 

Bug Fixes

    o   repeat.data(times=1,...) now produces valid output.

                 Changes in version 1.9.26 (2019-04-24)                 

Bug Fixes

    o   In the compute.pigengene function, if a module has only one
	gene, its name is now not omitted in the csv file.

                 Changes in version 1.9.24 (2019-04-24)                 

Changes in existing functions

    o   An object of pigengene-class can now have a heavyToLow
	attribute.

                 Changes in version 1.9.20 (2019-04-12)                 

Changes in existing functions

    o   In the compute.pigengene function, the columns of Data and
	names of modules can now differ.

                 Changes in version 1.9.14 (2019-02-12)                 

Changes in existing functions

    o   The dOrderByW argument is now added for the compute.pigengene
	function.

                 Changes in version 1.9.8 (2018-11-22)                  

Changes in existing functions

    o   All of the learn.bn function can now be set from
	one.step.pigengene through bnArgs.

                 Changes in version 1.9.4 (2018-11-16)                  

Changes in existing functions

    o   gene.mapping can now output multiple conventions.

                 Changes in version 1.7.2 (2018-05-22)                  

General

    o   The version of the package C50 is now required to be at least
	0.1.2, which exports the as.party.C5.0() function.

                 Changes in version 1.5.22 (2018-04-28)                 

Bug Fixes

    o   stats::cor is used in compute.pigengene and draw.cor functions.
	See the NAMESPACE for the important reason.

                 Changes in version 1.5.9 (2018-03-12)                  

General

    o   cor is imported from WGCNA, but not from stats, because WGCNA
	does not call the cor function properly.

Changes in existing functions

    o   RsquaredCut is added to the arguments of the one.step.pigengene
	function.

                 Changes in version 1.5.6 (2018-01-19)                  

Changes in existing functions

    o   In the get.fitted.leaf function, the function
	C50:::as.party.C5.0 is used, which used to be exported in the
	previous versions of C50, but not in version 0.1.1.

                 Changes in version 1.5.2 (2017-11-10)                  

New functions

    o   The check.nas function is now exported.

                 Changes in version 1.3.8 (2017-09-13)                  

Changes in existing functions

    o   Order of conditions in pheatmap.type can now be determined by
	the user.

                 Changes in version 1.3.6 (2017-08-20)                  

Changes in existing functions

    o   A bug in gene.mapping () function fixed to better map probe
	IDs.

                 Changes in version 1.3.4 (2017-07-31)                  

Changes in existing functions

    o   The doTranspose argument added to the heatmap.type() function.

                 Changes in version 1.1.14 (2017-05-10)                 

Changes in existing functions

    o   A bug in the module.heatmap() function fixed.

                 Changes in version 1.1.12 (2017-04-15)                 

Changes in existing functions

    o   The mouseHomologFilter argument is added to the unexported
	furntion hu.mouse() with a default value of
	"with_mmusculus_homolog". This is now compatible with
	biomaRt_2.30.0, it used to be "with_homolog_mmus" in older
	versions of biomaRt.

                 Changes in version 1.1.10 (2017-03-30)                 

Changes in existing functions

    o   Checking the pigengene input of module.heatmap().

    o   Issues in the balance() function (not exported) where Labels is
	a factor are resolved. Also, if all sampls have the same size,
	oversampling is automatically turned off.

    o   If Labels is a factor, it is now converted to a character
	vector in check. pigengene.input().

                 Changes in version 1.1.6 (2017-03-27)                  

Changes in existing functions

    o   The module.heatmap() function now has the doAddEigengene and
	scalePngs arguments.

    o   The compute.pigengene() function now reports also the size of
	modules in the pigengene_pvalue.csv output file.

                Changes in version 0.99.25 (2016-10-02)                 

Changes in existing functions

    o   The compute.pigengene() function now uses welch.pvalue()
	instead of pvalues.manov().

                 Changes in version 0.99.8 (2016-05-18)                 

General

    o   Under review by Bioconductor.

    o   Created.